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Modeling of the HS/heparin binding sites on SAA. A, the amino acid sequence of mouse SAA1.1, with conserved residues marked in blue. The central domain, which comprises the pH-dependent HS/heparin binding site, is underlined. B, a model of the domain was generated by homology software (see “Experimental Procedures”). The domain was found to have a length of 25 Å. Conserved residues are displayed with ball-and-stick models in blue. The basic amino acids that are aligned in the same direction in space, and therefore expected to be critical for HS/heparin binding, are marked in magenta. The histidine 36 residue, which accounts for the pH-dependent HS/heparin and HDL-SAA interaction (10), is located in the center of the domain. C, structure of a heparin 6-mer is shown (32 Å) (PDB ID: 1HPN (32)).

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